ETEC Carriage in Bangladesh: Case-Control Gut Metagenomics
48 faecal metagenome samples from asymptomatic and symptomatic ETEC-infected individuals in Bangladesh, comparing gut microbiomes in a case-control design to explore links between microbiota and symptomatic versus asymptomatic infection. machine-written summary
48 samples · 48 runs · BD · Age unknown · 2018 · 3.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 48 sample values (subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 96 sample values (location locality, location site) · PMC9239084 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 144 sample values (country, health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 45 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 48 | 100% | 48 | |||
| health_condition | 48 | 100% | 48 | |||
| subject_id | 48 | 100% | 48 | |||
| detailed_location | 48 | 100% | ||||
| health_condition_detail | 48 | 100% | 48 | |||
| location_locality | 48 | 100% | 48 | |||
| location_site | 48 | 100% | 48 |
- Microbiome Profiling of Enterotoxigenic Escherichia coli (ETEC) Carriers Highlights Signature Differences between Symptomatic and Asymptomatic Individuals. 2022 PMID 35536001 PMC9239084 own_data
Archive description
Infection with the same gut pathogen results in symptomatic diarrhoeal disease in some individuals while others carry the pathogen asymptomatically. While this could be due to genetic differences at the host level, the role of microbiota and interaction of the pathogen with its microbiome in the gut cannot be ignored. In collaboration with icddr,b in Dhaka, Bangladesh we have extracted metagenomic DNA from the faeces of asymptomatic and symptomatic carriers of Enterotoxigenic E coli (ETEC). Asymptomatic and symptomatic ETEC infected subjects have been sampled and DNA from their faeces will be subjected to shotgun metagenomic sequencing to identify the difference in their gut microbiomes. This will help us establish symptomatic disease-microbiota association, if any. We expect the results to show clear diversity patterns linked to either asymtpmatic and symptomatic carriage of ETEC.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “gut metagenome”
- body site study.description · “extracted metagenomic DNA from the faeces”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104166743 | country | BD | R2 | 0.75 | external.gmrepo source | country: Bangladesh |
| SAMEA104166743 | health_condition | gi_infection_or_diarrhoea | R2 | 0.75 | external.gmrepo source | phenotype: Escherichia coli Infections |
| SAMEA104166743 | health_condition_detail | Escherichia coli Infections | R2 | 0.75 | external.gmrepo source | phenotype: Escherichia coli Infections |
| SAMEA104166743 | location_locality | Dhaka | R3 | 0.60 | paper.fulltext.results | International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) in Dhaka |
| SAMEA104166743 | location_site | International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) | R3 | 0.70 | paper.fulltext.methods | International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) |
| SAMEA104166743 | subject_id | AM7024391 | R1 | 0.85 | sample.attr.subject_id | AM7024391 |
Sequencing
48 runs over 48 samples · mean 3.92 Gbp per run (median 3.95 Gbp, total 188.34 Gbp; 48 runs with a base count) · layout PAIRED 48 · platform ILLUMINA 48 · models Illumina HiSeq 2500 (48) · 94% of runs with a Sandpiper profile · first public 2018-09-12 – 2020-01-28
Authors (10)
Higginson EE first · Sayeed MA · Pereira Dias J · Shetty V · Ballal M · Srivastava SK · Willis I · Qadri F · Dougan G · Mutreja A last
Downloads
PRJEB21793.csv.gz (2.3 KB) · parquet (71.8 KB) — all 48 samples, every field with route and confidence · PRJEB21793_determinations.csv.gz (2.9 KB) — 288 evidence rows